Oropharyngeal Swab Specimens Research Articles

Comparative analysis of oropharyngeal microbiota in healthcare workers post-COVID-19.

To date, more than 770 million individuals have become coronavirus disease 2019 (COVID-19) convalescents worldwide. Emerging evidence highlights the influence of COVID-19 on the oral microbiome during both acute and convalescent disease phases. Front-line healthcare workers are at an elevated risk of exposure to viral infections, and the effects of COVID-19 on their oral microbiome remain relatively unexplored. Oropharyngeal swab specimens, collected one month after a negative COVID-19 test from a cohort comprising 55 healthcare workers, underwent 16S rRNA sequencing. We conducted a comparative analysis between this post-COVID-19 cohort and the pre-infection dataset from the same participants. Community composition analysis, indicator species analysis, alpha diversity assessment, beta diversity exploration, and functional prediction were evaluated. The Shannon and Simpson indexes of the oral microbial community declined significantly in the post-COVID-19 group when compared with the pre-infection cohort. Moreover, there was clear intergroup clustering between the two groups. In the post-COVID-19 group, the phylum Firmicutes showed a significant increase. Further, there were clear differences in relative abundance of several bacterial genera in contrast with the pre-infection group, including Streptococcus, Gemella, Granulicatella, Capnocytophaga, Leptotrichia, Fusobacterium, and Prevotella. We identified Gemella enrichment in the post-COVID-19 group, potentially serving as a recovery period performance indicator. Functional prediction revealed lipopolysaccharide biosynthesis downregulation in the post-COVID-19 group, an outcome with host inflammatory response modulation and innate defence mechanism implications. During the recovery phase of COVID-19, the oral microbiome diversity of front-line healthcare workers failed to fully return to its pre-infection state. Despite the negative COVID-19 test result one month later, notable disparities persisted in the composition and functional attributes of the oral microbiota.

Performance evaluation of influenza a rapid antigen test and PCR among nasopharyngeal and oropharyngeal samples

ObjectivesRapid antigen test (RAT) and polymerase chain reaction (PCR) using nasopharyngeal (NP) or oropharyngeal (OP) swab specimens are the two main testing techniques used for laboratory diagnosis of influenza in clinical practice. However, performance variations have been observed not only between techniques, but also between different specimens. This study evaluated the differences in performance between specimens and testing techniques to identify the best combination in clinical practice. MethodsBoth NP and OP samples from suspected influenza patients collected in the 2023/4–2023/5 Flu-season in Xiamen, China, were tested for RAT and quantitative PCR. The testing performance of the different specimens and testing techniques were recorded and evaluated. ResultsCompared to PCR, RAT showed 58.9 % and 10.3 % sensitivity for NP and OP swabs, respectively. The Limit of Detection (LoD) was 28.71 the Median Tissue Culture Infectious Dose (TCID50)/mL. Compared with PCR using NP swabs, PCR with OP swabs showed 89.5 % sensitivity and 95.4 % specificity. ConclusionsThere were no significant differences in performance between the specimens when PCR was used to test for influenza. However, a decrease in sensitivity was observed when the RAT was used, regardless of the specimen type. Therefore, to avoid false-negative results, PCR may be a better choice when OP swabs are used as specimens. In contrast, NP swabs should be the recommended specimens for RAT.

Performance of the Xpert™ Mpox PCR assay with oropharyngeal, anorectal, and cutaneous lesion swab specimens

Anorectal and oropharyngeal exposures are implicated in sexual transmission of mpox, but authorized assays in the United States are only validated with cutaneous lesion swabs. Diagnostic assays for anorectal and oropharyngeal swabs are needed to address potential future outbreaks. The Cepheid Xpert® Mpox is the first point-of-care assay to receive FDA emergency use authorization in the United States and would be a valuable tool for evaluating these sample types. Our exploratory study demonstrates 100 % positive agreement with our in-house PCR assay for natural positive anorectal and oropharyngeal specimens and 92 % sensitivity with low-positive spiked specimens. The Xpert® assay detected viral DNA in specimens not detected by our reference PCR assay from four participants with mpox DNA at other sites, suggesting it may be more sensitive at low viral loads. In conclusion, the validation of the Xpert® for oropharyngeal and anorectal sample types can be rapidly achieved if clinical need returns and prospective samples become available.

Avian influenza A(H5) virus circulation in live bird markets in Vietnam, 2017-2022.

Highly pathogenic avian influenza A(H5) human infections are a global concern, with many A(H5) human cases detected in Vietnam, including a case in October 2022. Using avian influenza virus surveillance from March 2017-September 2022, we described the percent of pooled samples that were positive for avian influenza A, A(H5), A(H5N1), A(H5N6), and A(H5N8) viruses in live bird markets (LBMs) in Vietnam. Monthly at each LBM, 30 poultry oropharyngeal swab specimens and five environmental samples were collected. Samples were pooled in groups of five and tested for influenza A, A(H5), A(H5N1), A(H5N6), and A(H5N8) viruses by real-time reverse-transcription polymerase chain reaction. Trends in the percent of pooled samples that were positive for avian influenza were summarized by LBM characteristics and time and compared with the number of passively detected avian influenza outbreaks using Spearman's rank correlation. A total of 25,774 pooled samples were collected through active surveillance at 167 LBMs in 24 provinces; 36.9% of pooled samples were positive for influenza A, 3.6% A(H5), 1.9% A(H5N1), 1.1% A(H5N6), and 0.2% A(H5N8). Influenza A(H5) viruses were identified January-December and at least once in 91.7% of sampled provinces. In 246 A(H5) outbreaks in poultry; 20.3% were influenza A(H5N1), 60.2% A(H5N6), and 19.5% A(H5N8); outbreaks did not correlate with active surveillance. In Vietnam, influenza A(H5) viruses were detected by active surveillance in LBMs year-round and in most provinces sampled. In addition to outbreak reporting, active surveillance for A(H5) viruses in settings with high potential for animal-to-human spillover can provide situational awareness.

1022. Detection of Mpox virus with the Cepheid Xpert Mpox assay in oropharyngeal, anorectal and cutaneous lesion swab specimens

Abstract Background The global spread of Mpox in 2022 largely affected men who have sex with men and exposures via the oropharynx and anorectum are thought to contribute to sexual transmission. New molecular platforms including point-of-care assays for detection of Mpox DNA from cutaneous lesion samples have received emergency use authorization in the United States but these technologies are not validated for use with other sample types, including oropharyngeal or anorectal swabs. Methods Anorectal, oropharyngeal and cutaneous lesion swabs swabs were initially collected and frozen dry at -80C during clinical evaluation for suspected Mpox at a large HIV care center in Atlanta, GA. Swabs were thawed to room temperature and eluted in 3 mL of transport medium prior to testing on the Cepheid Xpert platform, which was performed according to the assay's instructions for use. DNA extracted from 140 μL of the same sample was used for non-variola orthopoxvirus (E9L-NVAR) PCR as a reference test and RNaseP PCR as a sample adequacy control. Results Positive agreement between the Xpert Mpox assay and in-house PCR was 100% for 9 cutaneous lesion swabs, 8 oropharyngeal swabs, and 5 anorectal swabs (see Figure). There were no false-negative results returned by the Xpert. Overall negative agreement was 86.7% (26/30). The Xpert assay was positive in 6 specimens where viral DNA was not detected by the NVOG assay including two specimens that also did not have detectable RNAseP. 4 of these 6 specimens with discordant results were from patients with viral DNA detected at other anatomic sites. Results of the Xpert Mpox assay, NVAR PCR, and sample adequacy controls for cutaneous lesion, oropharyngeal and anorectal specimens. The Xpert assay was positive for 100% of specimens when the non-variola orthopoxvirus (NVAR) target detected by our reference assay and there were no false negative results. The Xpert assay also detected viral targets in 6 specimens where no viral DNA was detected by the NVAR assay. However, four of these specimens were collected from patients with Mpox DNA detected at other anatomic sites. Conclusion The Xpert Mpox assay had perfect positive agreement with the NVAR PCR assay in anorectal, oropharyngeal and cutaneous lesion swab specimens suggesting it has high sensitivity for diagnosis of Mpox infection at the point-of-care, including with not-yet validated sample types. Specificity of the assay is difficult to estimate from our data, as a likely explanation of our results is that the Xpert Mpox assay has a lower limit of detection compared to our reference assay. This is evidenced by detection of Mpox DNA with high Ct values in samples from patients with viral DNA confirmed by both assays at other anatomic sites. The Xpert Mpox assay can be expected to perform well with oropharyngeal and anorectal swab specimens in clinical settings. Disclosures Jonathan Colasanti, MD, MSPH, DKB MED LLC: Honoraria|Prime Education LLC: Advisor/Consultant

Evaluation of a novel lyophilized-pellet-based 2019-nCoV nucleic acid detection kit for the diagnosis of COVID-19.

The coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has swept the world and poses a serious threat to human health. In the post-pandemic-era, we must remain vigilant against the co-infection of SARS-CoV-2 and other respiratory viruses. More accurate and convenient detection methods are required for the diagnosis of SARS-CoV-2 due to its prolonged existence. In this study, the application value of a novel lyophilized-pellet-based 2019-nCoV nucleic acid diagnostic kit (PCoV-Kit) was evaluated by comparing it with a conventional liquid diagnostic kit (LCoV-Kit). We assessed the sensitivity, precision, accuracy, specificity, and amplification efficiency of PCoV-Kit and LCoV-Kit using diluted SARS-CoV-2 RNA reference materials. The results showed that both kits had high sensitivity, precision, accuracy, and specificity. A total of 2,033 oropharyngeal swab specimens collected during mass screening in Fuzhou in December 2022 were applied for the consistency analysis of the two reagents. In the detection of clinical oropharyngeal swab specimens, although the positive rate of PCoV-Kit (19.28%) was slightly lower than that of LCoV-Kit (20.86%), statistical analysis demonstrated a high degree of consistency between the test results obtained using both kit (χ2 = 1.57, P>0.05; Kappa coefficient = 0.90, 95%CI: 0.88-0.93). In conclusion, the use of lyophilized PCoV-Kit provides a non-inferior assay for the diagnosis of COVID-19.

Detection of Rotavirus in Respiratory Specimens From Bangladeshi Children Aged

To examine the potential for respiratory transmission of rotavirus, we systematically assessed if rotavirus RNA is detectable by real-time quantitative reverse transcription-polymerase chain reaction from nasal and oropharyngeal swab specimens of Bangladeshi children with acute rotavirus gastroenteritis. Forehead swabs were collected to assess skin contamination. Among 399 children aged <2 years hospitalized for gastroenteritis during peak rotavirus season, rotavirus RNA was detected in stool, oral, nasal and forehead swab specimens of 354 (89%). A subset was genotyped; genotype was concordant within a child's specimen set and several different genotypes were detected across children. These findings support possible respiratory transmission of rotavirus and warrant further investigation.

Daily SARS-CoV-2 Nasal Antigen Tests Miss Infected and Presumably Infectious People Due to Viral Load Differences among Specimen Types.

In a recent household transmission study of SARS-CoV-2, we found extreme differences in SARS-CoV-2 viral loads among paired saliva, anterior nares swab (ANS), and oropharyngeal swab specimens collected from the same time point. We hypothesized these differences may hinder low-analytical-sensitivity assays (including antigen rapid diagnostic tests [Ag-RDTs]) by using a single specimen type (e.g., ANS) from reliably detecting infected and infectious individuals. We evaluated daily at-home ANS Ag-RDTs (Quidel QuickVue) in a cross-sectional analysis of 228 individuals and a longitudinal analysis (throughout infection) of 17 individuals enrolled early in the course of infection. Ag-RDT results were compared to reverse transcription-quantitative PCR (RT-qPCR) results and high, presumably infectious viral loads (in each, or any, specimen type). The ANS Ag-RDT correctly detected only 44% of time points from infected individuals on cross-sectional analysis, and this population had an inferred limit of detection of 7.6 × 106 copies/mL. From the longitudinal cohort, daily Ag-RDT clinical sensitivity was very low (<3%) during the early, preinfectious period of the infection. Further, the Ag-RDT detected ≤63% of presumably infectious time points. The poor observed clinical sensitivity of the Ag-RDT was similar to what was predicted based on quantitative ANS viral loads and the inferred limit of detection of the ANS Ag-RDT being evaluated, indicating high-quality self-sampling. Nasal Ag-RDTs, even when used daily, can miss individuals infected with the Omicron variant and even those presumably infectious. Evaluations of Ag-RDTs for detection of infected or infectious individuals should be compared with a composite (multispecimen) infection status to correctly assess performance. IMPORTANCE We reveal three findings from a longitudinal study of daily nasal antigen rapid diagnostic test (Ag-RDT) evaluated against SARS-CoV-2 viral load quantification in three specimen types (saliva, nasal swab, and throat swab) in participants enrolled at the incidence of infection. First, the evaluated Ag-RDT showed low (44%) clinical sensitivity for detecting infected persons at all infection stages. Second, the Ag-RDT poorly detected (≤63%) time points that participants had high and presumably infectious viral loads in at least one specimen type. This poor clinical sensitivity to detect infectious individuals is inconsistent with the commonly held view that daily Ag-RDTs have near-perfect detection of infectious individuals. Third, use of a combination nasal-throat specimen type was inferred by viral loads to significantly improve Ag-RDT performance to detect infectious individuals.

Metatranscriptomic analysis revealed Prevotella as a potential biomarker of oropharyngeal microbiomes in SARS-CoV-2 infection.

Disease severity and prognosis of coronavirus disease 2019 (COVID-19) disease with other viral infections can be affected by the oropharyngeal microbiome. However, limited research had been carried out to uncover how these diseases are differentially affected by the oropharyngeal microbiome of the patient. Here, we aimed to explore the characteristics of the oropharyngeal microbiota of COVID-19 patients and compare them with those of patients with similar symptoms. COVID-19 was diagnosed in patients through the detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by quantitative reverse transcription polymerase chain reaction (RT-qPCR). Characterization of the oropharyngeal microbiome was performed by metatranscriptomic sequencing analyses of oropharyngeal swab specimens from 144 COVID-19 patients, 100 patients infected with other viruses, and 40 healthy volunteers. The oropharyngeal microbiome diversity in patients with SARS-CoV-2 infection was different from that of patients with other infections. Prevotella and Aspergillus could play a role in the differentiation between patients with SARS-CoV-2 infection and patients with other infections. Prevotella could also influence the prognosis of COVID-19 through a mechanism that potentially involved the sphingolipid metabolism regulation pathway. The oropharyngeal microbiome characterization was different between SARS-CoV-2 infection and infections caused by other viruses. Prevotella could act as a biomarker for COVID-19 diagnosis and of host immune response evaluation in SARS-CoV-2 infection. In addition, the cross-talk among Prevotella, SARS-CoV-2, and sphingolipid metabolism pathways could provide a basis for the precise diagnosis, prevention, control, and treatment of COVID-19.

Adequacy of using a single nasal swab for rapid influenza diagnostic testing, PCR, and whole genome sequencing.

Rapid influenza diagnostic tests (RIDT) demonstrate varying sensitivities, often necessitating reverse transcriptase polymerase chain reaction (RT-PCR) to confirm results. The two methods generally require separate specimens. Using the same anterior nasal swab for both RIDT and molecular confirmation would reduce cost and waste and increase patient comfort. The aim of this study was to determine if RIDT residual nasal swab (rNS) specimens are adequate for RT-PCR and whole genome sequencing (WGS). We performed RT-PCR and WGS on paired rNS and nasopharyngeal or oropharyngeal (NP/OP) swab specimens that were collected from primary care patients across all ages. We randomly selected 199 and 40 paired specimens for RT-PCR and WGS, respectively, from the 962 paired surveillance specimens collected during the 2014-2015 influenza season. Sensitivity and specificity for rNS specimens were 81.3% and 96.7%, respectively, as compared to NP/OP specimens. The mean cycle threshold (Ct) value for the NP/OP specimen was significantly lower when the paired specimens were both positive than when the NP/OP swab was positive and the nasal swab was negative (25.5 vs 29.5; p<0.001). Genomic information was extracted from all 40 rNS specimens and 37 of the 40 NP/OP specimens. Complete WGS reads were available for 67.5% (14 influenza A; 13 influenza B) of the rNS specimens and 59.5% (14 influenza A; 8 influenza B) of the NP/OP specimens. It is feasible to use a single anterior nasal swab for RIDT followed by RT-PCR and/or WGS. This approach may be appropriate in situations where training and supplies are limited. Additional studies are needed to determine if residual nasal swabs from other rapid diagnostic tests produce similar results.

Higher SARS-CoV-2 detection of oropharyngeal compared with nasopharyngeal or saliva specimen for molecular testing: a multicentre randomised comparative accuracy study

BackgroundTesting is critical for detecting SARS-CoV-2 infection, but the best sampling method remains unclear.ObjectivesTo determine whether nasopharyngeal swab (NPS), oropharyngeal swab (OPS) or saliva specimen collection has the highest detection...

Azithromycin alters spatial and temporal dynamics of airway microbiota in idiopathic pulmonary fibrosis.

High bacterial burden in the lung microbiota predicts progression of idiopathic pulmonary fibrosis (IPF). Azithromycin (AZT) is a macrolide antibiotic known to alter the lung microbiota in several chronic pulmonary diseases, and observational studies have shown a positive effect of AZT on mortality and hospitalisation rate in IPF. However, the effect of AZT on the lung microbiota in IPF remains unknown. We sought to determine the impact of a 3-month course of AZT on the lung microbiota in IPF. We assessed sputum and oropharyngeal swab specimens from 24 adults with IPF included in a randomised controlled crossover trial of oral AZT 500 mg 3 times per week. 16S rRNA gene amplicon sequencing and quantitative PCR (qPCR) were performed to assess bacterial communities. Antibiotic resistance genes (ARGs) were assessed using real-time qPCR. AZT significantly decreased community diversity with a stronger and more persistent effect in the lower airways (sputum). AZT treatment altered the temporal kinetics of the upper (oropharyngeal swab) and lower airway microbiota, increasing community similarity between the two sites for 1 month after macrolide cessation. Patients with an increase in ARG carriage had lower bacterial density and enrichment of the genus Streptococcus. In contrast, patients with more stable ARG carriage had higher bacterial density and enrichment in Prevotella. AZT caused sustained changes in the diversity and composition of the upper and lower airway microbiota in IPF, with effects on the temporal and spatial dynamics between the two sites.

Epidemiology of respiratory syncytial virus in hospitalized children with community-acquired pneumonia in Guangzhou: a 10-year study.

Respiratory syncytial virus (RSV) is one of the most common virus causing community-acquired pneumonia (CAP) in children. To guide the prevention, diagnosis and treatment of RSV, we aimed to analyze the epidemiology of RSV in hospitalized children with CAP. A total of 9,837 hospitalized children (≤14 years old) with CAP from January 2010 to December 2019 were reviewed. Using the real-time polymerase chain reaction (RT-PCR), the oropharyngeal swab specimens were collected and tested for RSV, influenza virus A (INFA), influenza virus B (INFB), parainfluenza virus (PIV), enterovirus (EV), coronavirus (CoV), human metapneumovirus (HMPV), human bocavirus (HBoV), human rhinovirus (HRV), and adenovirus (ADV) for each patient. The detection rate of RSV was 15.3% (1,507/9,837). From 2010 to 2019, the RSV detection rate showed a wavy change (χ2=166.982, P<0.001), with the highest detection rate in 2011 (158/636, 24.8%). RSV can be detected throughout the year, with the highest detection rate in February (123/482, 25.5%). Children younger than 0.5 years old had the highest detection rate (410/1,671, 24.5%). The detection rate of RSV in male children (1,024/6,226, 16.4%) was higher than that in female children (483/3,611, 13.4%) (P<0.001). A proportion of 17.7% (266/1,507) of RSV positive cases were also co-infected with other viruses, and INFA (41/266, 15.4%) was the most common coinfection virus. After adjusting for potential confounders, the RSV-positive children were associated with increased risk of severe pneumonia [odds ratio (OR) 1.26, 95% confidence interval (CI): 1.04 to 1.53, P=0.019]. Moreover, children with severe pneumonia had significantly lower cycle threshold (CT) values of RSV than those without severe pneumonia (28.88±3.89 vs. 30.42±3.33, P<0.01). Patients with coinfection (38/266, 14.3%) had a higher risk of severe pneumonia than those without coinfection (142/1,241, 11.4%), but the difference was not statistically significant (OR 1.39, 95% CI: 0.94 to 2.05, P=0.101). The detection rate of RSV in CAP hospitalized children changed by years, months, ages, and sexes. CAP hospitalized children with RSV are more likely to develop severe pneumonia than those without RSV. Policy makers and doctors should make timely adjustments to prevention measures, medical resources and treatment options based on these epidemiological characteristics.

Laboratory diagnosis of COVID-19 cases from nasal and oropharyngeal swab specimens

Introduction: Indonesia first reported Covid-19 on March 2, 2020, which continued to increase and spread rapidly throughout Indonesia. WHO recommends molecular examinations for patients with suspected COVID-19 through molecular detection method or NAAT (Nucleic Acid Amplification Test), including Real Time-Polymerase Chain Reaction (RT-PCR) tests. This study aimed to describe the profile of RT-PCR test services on nasal and oropharyngeal swab specimens from patients treated at Dr. Pirngadi Hospital Medan and patients of primary health care (Puskesmas) or other hospitals referred for RT-PCR examination at the Laboratory of Dr. Pirngadi Hospital. Method: This was a retrospective, descriptive study using secondary data from medical records from August 2020 to July 2021. Using consecutive sampling, the study sample was all suspected and confirmed COVID-19 specimens collected at Dr. Pirngadi Hospital, Medan. All collected data were processed and analyzed using IBM SPSS version 20.0. Result: There were 7495 specimens of COVID-19 from Dr. Pirngadi Hospital from August 2020 to July 2021, of which 1264 (17%) were confirmed positive, and 6231 (83%) had negative results. Meanwhile, 12.274 specimens were obtained from primary health care or other hospitals, of which 2602 (2%) samples were confirmed positive, and 9672 (98%) had negative results. Based on sex, 884 men (44%) and 1108 women (56%) had confirmed COVID-19 cases. Conclusion: From August 2020 to July 2021, this study found 17% and 2% of confirmed COVID-19 cases at Dr. Pirngadi Hospital and primary health care or other hospitals, respectively. COVID-19-confirmed issues were more common in women.

Seroprevalence of anti-SARS-CoV-2 specific antibodies in vaccinated and vaccine naïve adult Nigerians.

Reports on the evaluation of immune responses to different COVID-19 vaccines are limited. Similarly, effects of age and gender have not been well explored as variables that could impact on the vaccine-induced antibody response. Therefore, seroprevalence of anti-SARS-CoV-2 specific antibodies in vaccinated and vaccine naïve adult Nigerians was determined in this study. A total of 141 adults were enrolled into this study. Presence or absence of SARS-CoV-2 infection was confirmed by real-time reverse-transcriptase polymerase-chain reaction (RT-PCR) assay on nasopharyngeal and oropharyngeal swab specimens. Anti-SARS-CoV-2 Specific IgG and IgM antibodies were qualitatively detected using a Rapid Diagnostic Test kit. Pre-vaccination, 77% of the study participants had never had PCR-confirmed COVID-19 test yet 66.7% of them were seropositive for SARS-CoV-2 antibodies. Of 111 COVID-19 vaccinated participants, 69.2% and 73.8% of them had SARS-CoV-2 specific IgG post-first and second doses of COVID-19 vaccine respectively. However, 23.1% and 21.4% of the participants who have had first and second doses respectively had no detectable anti-SARS-CoV-2 antibodies. The proportion of participants with SARS-CoV-2 specific IgG was insignificantly higher in those between the ages of 18-40 years and 41-59 years compared with individuals aged ≥60 years. No significant association was observed between gender and seropositivity for SARS-CoV-2 antibodies. There is high SARS-CoV-2 antibody seroprevalence among Nigerian adults who never had PCR-confirmed COVID-19. Also, there is the need for anti-SARS-CoV-2 antibodies screening post vaccination as this could be essential in achieving herd immunity. Age and gender do not seem to have significant association with seropositivity.

Performance Evaluation of Two Kinds of Rapid Antigen Test Kits for Detection of COVID-19 Infection.

The diagnostic standard for COVID-19 infection is real-time reverse transcription-polymerase chain reaction (rRT-PCR) of nasopharyngeal swab and oropharyngeal swab specimens. Rapid antigen tests are cheaper and easier to use than the rRT-PCR method. Although the COVID-19 pandemic is settling down, seasonal epi¬demic is expected. In this study, the performance of two rapid antigen test kits was evaluated based on rRT-PCR test results. A total of 346 residual samples was tested by the PowerChek SARS-CoV-2 Real-time PCR Kit or STAN-DARD M nCoV Real-Time-Detection kit, STANDARD Q COVID-19 Ag test kit (SQ RAT), and ND COVID-19 Ag test kit (ND RAT). Compared to rRT-PCR as the standard method, the SQ RAT test kit yielded 77.1% sensitivity (101/131) and 100% specificity (215/215), and the ND RAT yielded 89.3% sensitivity (117/131) and 100% specificity (215/ 215). Both RATs showed sensitivity greater than 85% in samples with RdRp gene Ct value less than 25. There was a false-negative case suspected of prozone phenomenon. Both RATs showed significant performance, but users should beware of the prozone phenomenon.

Metatranscriptomic Analysis Reveals Disordered Alterations in Oropharyngeal Microbiome during the Infection and Clearance Processes of SARS-CoV-2: A Warning for Secondary Infections

This study was conducted to investigate oropharyngeal microbiota alterations during the progression of coronavirus disease 2019 (COVID-19) by analyzing these alterations during the infection and clearance processes of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The diagnosis of COVID-19 was confirmed by using positive SARS-CoV-2 quantitative reverse transcription polymerase chain reaction (RT-qPCR). The alterations in abundance, diversity, and potential function of the oropharyngeal microbiome were identified using metatranscriptomic sequencing analyses of oropharyngeal swab specimens from 47 patients with COVID-19 (within a week after diagnosis and within two months after recovery from COVID-19) and 40 healthy individuals. As a result, in the infection process of SARS-CoV-2, compared to the healthy individuals, the relative abundances of Prevotella, Aspergillus, and Epstein-Barr virus were elevated; the alpha diversity was decreased; the beta diversity was disordered; the relative abundance of Gram-negative bacteria was increased; and the relative abundance of Gram-positive bacteria was decreased. After the clearance of SARS-CoV-2, compared to the healthy individuals and patients with COVID-19, the above disordered alterations persisted in the patients who had recovered from COVID-19 and did not return to the normal level observed in the healthy individuals. Additionally, the expressions of several antibiotic resistance genes (especially multi-drug resistance, glycopeptide, and tetracycline) in the patients with COVID-19 were higher than those in the healthy individuals. After SARS-CoV-2 was cleared, the expressions of these genes in the patients who had recovered from COVID-19 were lower than those in the patients with COVID-19, and they were different from those in the healthy individuals. In conclusion, our findings provide evidence that potential secondary infections with oropharyngeal bacteria, fungi, and viruses in patients who have recovered from COVID-19 should not be ignored; this evidence also highlights the clinical significance of the oropharyngeal microbiome in the early prevention of potential secondary infections of COVID-19 and suggests that it is imperative to choose appropriate antibiotics for subsequent bacterial secondary infection in patients with COVID-19.

Peptide-based direct electrochemical detection of receptor binding domains of SARS-CoV-2 spike protein in pristine samples

RNA isolation and amplification-free user-friendly detection of SARS-CoV-2 is the need of hour especially at resource limited settings. Herein, we devised the peptides of human angiotensin converting enzyme-2 (hACE-2) as bioreceptor at electrode interface for selective targeting of receptor binding domains (RBD) of SARS-CoV-2 spike protein (SP). Disposable carbon-screen printed electrode modified with methylene blue (MB) electroadsorbed graphene oxide (GO) has been constructed as cost-efficient and scalable platform for hACE-2 peptide-based SARS-CoV-2 detection. In silico molecular docking of customized 25 mer peptides with RBD of SARS-CoV-2 SP were validated by AutoDock CrankPep. N-terminal region of ACE-2 showed higher binding affinity of − 20.6 kcal/mol with 15 H-bond, 9 of which were < 3 Å. Electrochemical biosensing of different concentrations of SPs were determined by cyclic voltammetry (CV) and chronoamperometry (CA), enabling a limit of detection (LOD) of 0.58 pg/mL and 0.71 pg/mL, respectively. MB-GO devised hACE-2 peptide platform exert an enhanced current sensitivity of 0.0105 mA/pg mL−1 cm−2 (R2 = 0.9792) (CV) and 0.45 nA/pg mL−1 (R2 = 0.9570) (CA) against SP in the range of 1 pg/mL to 1 µg/mL. For clinical feasibility, nasopharyngeal and oropharyngeal swab specimens in viral transport medium were directly tested with the prepared peptide biosensor and validated with RT-PCR, promising for point-of-need analysis.

Occurrence of influenza and bacterial infections in cancer patients receiving radiotherapy in Ghana.

BackgroundInfluenza co-infection with bacteria is a leading cause of influenza-related deaths and severe respiratory infections, especially among high-risk groups like cancer patients undergoing treatment. However, acute respiratory infection (ARI)-like symptoms developed by upper-torso cancer (UTC) patients receiving radiotherapy are considered as side-effects of the radiation. Hence influenza and bacterial pathogens implicated in ARI are not investigated.MethodsThis prospective cohort study examined 85 in-patients with upper-torso cancers undergoing radiotherapy at the National Radiotherapy, Oncology and Nuclear Medicine Centre (NRONMC) of Korle-Bu Teaching Hospital (KBTH) in Accra, Ghana. Eligible patients who consented were recruited into the study from September 2018 to April 2019. Influenza viruses A and B in addition to the following bacteria species Streptococcus pneumonia, Haemophilus influenzae, Neisseria meningitidis and Staphylococcus aureus were detected from oropharyngeal and nasopharyngeal swab specimens collected at three different time points. Presence of respiratory pathogens were investigated by influenza virus isolation in cell culture, bacterial culture, polymerase chain reaction (PCR) and next generation sequencing (NGS) assays.ResultsOf the 85 eligible participants enrolled into the study, 87% were females. Participants were 17 to 77 years old, with a median age of 49 years. Most of the participants (88%) enrolled had at least one pathogen present. The most prevalent pathogen was N. meningitidis (63.4%), followed by H. influenzae (48.8%), Influenza viruses A and B (32.9%), S. pneumoniae (32.9%) and S. aureus (12.2%). Approximately, 65% of these participants developed ARI-like symptoms. Participants with previous episodes of ARI, did not live alone, HNC and total radiation less than 50 Gy were significantly associated with ARI. All treatment forms were also significantly associated with ARI.ConclusionData generated from the study suggests that ARI-like symptoms observed among UTC patients receiving radiotherapy in Ghana, could be due to influenza and bacterial single and co-infections in addition to risk factors and not solely the side-effects of radiation as perceived. These findings will be prime importance for diagnosis, prevention, treatment and control for cancer patients who present with such episodes during treatment.

A reverse-transcription droplet digital PCR assay to detect and quantify SARS-CoV-2 RNA in upper respiratory tract specimens.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a positive-sense, single-stranded RNA virus that causes coronavirus disease 2019 (COVID-19). Symptoms are variable and range from asymptomatic or mild to severe (i.e., pneumonia) in both healthy and immunocompromised patients. We developed a reverse-transcription droplet digital PCR (RT-ddPCR) assay for quantification of SARS-CoV-2 RNA in clinical nasopharyngeal and oropharyngeal swab specimens and evaluated the assay, including reproducibility, agreement of results, analytical measurement range, linearity, analytical sensitivity, and analytical specificity. This quantitative assay had a LoD of 218 copies/mL of viral transport media, with a linear quantification range from 500 to 5,000,000 copies/mL (R2 of 0.9817 and 0.9853 for N1 and N2 targets, respectively). Qualitative agreement of categorical results was 90.5% (57/63) between the reference and RT-ddPCR assays. Quantitative agreement between the two assays showed correlation, with R2 of 0.9726 and 0.9713 for N1 and N2 targets, respectively. No cross-reactivity with common coronavirus strains was detected. This SARS-CoV-2 quantitative RT-ddPCR assay may be a useful tool for a variety of applications including identification of patients with low viral load and serial monitoring of viral load in respiratory tracts specimens of patients for evaluation of the efficacy of therapy for COVID-19.